[gmx-users] Problems with umbrella sampling

[Amir Marcovitz]

Thanks Justin,

it seems to help, i have another general question that you might help me
with:

should i define the distances for the umbrella sampling run in some file and
then run it?(i saw something about  *.ppa file but couldn't find any further
instructions in the mannual..)
will this file apply for the WHAM analysis after the run?

thanks,
Amir

On Mon, Dec 28, 2009 at 6:14 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Amir Marcovitz wrote:
>
>> Hi,
>>  my system is constructed of 2 parallel plates in a box with solvent. each
>> plate is made of 36 atoms which are positively charged on one of them (SRP)
>> and negatively charged on the other plate (SRN).
>>  i want to perform a simulation with umbrella sampling between the 2 so i
>> defined the pulling section parameters in the .mdp parameter file as
>> following:
>>  ; COM PULLING         ; Pull type: no, umbrella, constraint or
>> constant_force
>> pull                     = umbrella
>> ; Pull geometry: distance, direction, cylinder or position
>> pull_geometry            = distance
>> ; Select components for the pull vector. default: Y Y Y
>> pull_dim                 = Y Y Y
>> ; Cylinder radius for dynamic reaction force groups (nm)
>> pull_r1                  = 1
>> ; Switch from r1 to r0 in case of dynamic reaction force
>> pull_r0                  = 1.5
>> pull_constr_tol          = 1e-06
>> pull_start               = no
>> pull_nstxout             = 10
>> pull_nstfout             = 1
>> ; Number of pull groups
>> pull_ngroups             = 2
>> ; Group name, weight (default all 1), vector, init, rate (nm/ps),
>> kJ/(mol*nm^2)
>> pull_group0              = SRP
>> pull_weights0            = 1
>> pull_pbcatom0            = 0
>> pull_group1              = SRN
>> pull_weights1            = 1
>> pull_pbcatom1            = 0
>> pull_vec1                = 0.0 1.0 0.0
>> pull_init1               = 1.5
>> pull_rate1               = 0
>> pull_k1                  = 1
>> pull_kB1                 = 0
>>  when proccesing the file with grompp i get the following error:
>>  *Fatal error:
>> Number of weights (1) for pull group 0 'SRP' does not match the number of
>> atoms (36)*
>>  is someone recognizing my mistake?
>>
>
> Please refer to the manual (manual.gromacs.org is quite handy), you will
> find:
>
> "Optional relative weights which are multiplied with the masses of the
> atoms to give the total weight for the COM. The number should be 0, meaning
> all 1, or the number of atoms in the pull group."
>
> I also think your value for pull_ngroup is wrong.  It appears you are
> pulling SRN with respect to SRP, so you only have one pull group, not two.
>
> -Justin
>
>  does someone has an experience with umbrella sampling in GROMACS?
>>  thanks'
>> amir
>> *
>> *
>>
>>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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